Chronic Pelvic Pain Syndrome (CPPS) is a prevalent multifactorial disorder with variable and often disappointing response to therapy. There is evidence for infection, inflammation and neuromuscular spasm as the underlying cause in different patients despite identical clinical presentation. Large multicenter clinical trials are required to help delineate effective therapies and to identify which patients have the highest chance of success for a particular intervention. The Chronic Prostatitis Clinic at the Cleveland Clinic Florida has a high volume of patients, both newly diagnosed and longstanding. We have done numerous clinical trials in chronic prostatitis with rapid enrolment, 100% accrual of set targets and high rates of retention. We have a team of clinical specialists in allied fields important to the understanding of this condition, including experts in erectile dysfunction, rectal dysfunction, chronic pain management, complementary therapies (acupuncture, phytotherapy) and neuropsychology. We also maintain a basic science laboratory which would be equipped to perform any necessary molecular or biochemical ancillary studies such as real time PCR, oxidative stress markers, cytokines and genetic polymorphisms. Through our participation in the CPCRN and first NIH chronic prostatitis randomized clinical trial, we have demonstrated the ability to work collaboratively and to participate in study design and execution. As an example of a potential clinical trial, a study of water induced thermotherapy is outlined.